===============================
R CMD BUILD
===============================
* checking for file ‘dreamlet/DESCRIPTION’ ... OK
* preparing ‘dreamlet’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
Loading required namespace: dreamlet
Warning: replacing previous import ‘SingleCellExperiment::cpm’ by ‘edgeR::cpm’ when loading ‘dreamlet’
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘dreamlet’
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘zenith’
* saving partial Rd database
* creating vignettes ... ERROR
TIMEOUT: R CMD build exceeded 15 mins
===============================
R CMD BUILD
===============================
* checking for file ‘dreamlet/DESCRIPTION’ ... OK
* preparing ‘dreamlet’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to process help pages
Loading required namespace: dreamlet
Warning: replacing previous import ‘SingleCellExperiment::cpm’ by ‘edgeR::cpm’ when loading ‘dreamlet’
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘dreamlet’
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘zenith’
* saving partial Rd database
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘dreamlet_0.99.1.tar.gz’
===============================
BiocCheckGitClone('dreamlet')
===============================
─ BiocCheckVersion: 1.35.14
─ BiocVersion: 3.17
─ Package: dreamlet
─ PackageVersion: 0.99.1
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2955/dreamlet_20230323125331/dreamlet
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2955/dreamlet_20230323125331/dreamlet.Rcheck’
* using R Under development (unstable) (2023-03-16 r83996)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘dreamlet/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘dreamlet’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘dreamlet’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘SingleCellExperiment::cpm’ by ‘edgeR::cpm’ when loading ‘dreamlet’
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘dreamlet’
See ‘/home/pkgbuild/packagebuilder/workers/jobs/2955/dreamlet_20230323125331/dreamlet.Rcheck/00install.out’ for details.
* used C++ compiler: ‘g++ (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking C++ specification ... NOTE
Specified C++11: please drop specification unless essential
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [37s/37s] OK
* checking Rd files ... [11s/11s] WARNING
prepare_Rd: replacing previous import ‘SingleCellExperiment::cpm’ by ‘edgeR::cpm’ when loading ‘dreamlet’
prepare_Rd: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘dreamlet’
prepare_Rd: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘zenith’
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... [237s/237s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
run_mash 74.906 0.480 75.362
as.dreamletResult 49.421 1.859 51.286
fitVarPart 10.144 0.056 10.202
sortCols-method 9.807 0.052 9.860
plotVarPart-methods 9.697 0.020 9.718
plotPercentBars-methods 9.501 0.112 9.614
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [30s/42s]
[31s/43s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [3s/3s] OK
* DONE
Status: 2 WARNINGs, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2955/dreamlet_20230323125331/dreamlet.Rcheck/00check.log’
for details.
===============================
BiocCheck('dreamlet_0.99.1.tar.gz')
===============================
─ BiocCheckVersion: 1.35.14
─ BiocVersion: 3.17
─ Package: dreamlet
─ PackageVersion: 0.99.1
─ sourceDir: /tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet
─ installDir: /tmp/RtmpvH1yCE/file2494557b7c092b
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2955/dreamlet_20230323125331/dreamlet.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
* NOTE: Update R version dependency from 4.2.0 to 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
* NOTE: Consider adding these automatically suggested biocViews:
Sequencing, Microarray, ImmunoOncology
Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
Warning in tools::parse_Rd(infile) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/run_mash.Rd:104: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(infile) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
* Checking for library/require of dreamlet...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid using '=' for assignment and use '<-' instead
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 19 functions greater than 50 lines.
* Checking man page documentation...
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/run_mash.Rd:104: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning: replacing previous import ‘SingleCellExperiment::cpm’ by ‘edgeR::cpm’ when loading ‘dreamlet’
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘dreamlet’
Warning: replacing previous import ‘limma::topTable’ by ‘variancePartition::topTable’ when loading ‘zenith’
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/run_mash.Rd:104: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/run_mash.Rd:21: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/run_mash.Rd:23: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/run_mash.Rd:104: unknown macro '\insertAllCited'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpvH1yCE/file2494557a039ea8/dreamlet/man/zenith_gsa-methods.Rd:56: unknown macro '\insertCite'
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 386 lines (4%) are > 80 characters
long.
* NOTE: Consider 4 spaces instead of tabs; 1912 lines (20%) contain
tabs.
* NOTE: Consider multiples of 4 spaces for line indents; 505 lines
(5%) are not.
See https://contributions.bioconductor.org/r-code.html
See styler package: https://cran.r-project.org/package=styler as
described in the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 11 NOTES
See the dreamlet.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.